title: Analysis of long non-coding RNA expression profiles in gastric cancer.
abstract: OBJECTIVE
  To investigate the expression patterns of long non-coding RNAs (lncRNAs) in gastric cancer.
  
  
  METHODS
  Two publicly available human exon arrays for gastric cancer and data for the corresponding normal tissue were downloaded from the Gene Expression Omnibus (GEO). We re-annotated the probes of the human exon arrays and retained the probes uniquely mapping to lncRNAs at the gene level. LncRNA expression profiles were generated by using robust multi-array average method in affymetrix power tools. The normalized data were then analyzed with a Bioconductor package linear models for microarray data and genes with adjusted P-values below 0.01 were considered differentially expressed. An independent data set was used to validate the results.
  
  
  RESULTS
  With the computational pipeline established to re-annotate over 6.5 million probes of the Affymetrix Human Exon 1.0 ST array, we identified 136053 probes uniquely mapping to lncRNAs at the gene level. These probes correspond to 9294 lncRNAs, covering nearly 76% of the GENCODE lncRNA data set. By analyzing GSE27342 consisting of 80 paired gastric cancer and normal adjacent tissue samples, we identified 88 lncRNAs that were differentially expressed in gastric cancer, some of which have been reported to play a role in cancer, such as LINC00152, taurine upregulated 1, urothelial cancer associated 1, Pvt1 oncogene, small nucleolar RNA host gene 1 and LINC00261. In the validation data set GSE33335, 59% of these differentially expressed lncRNAs showed significant expression changes (adjusted P-value < 0.01) with the same direction.
  
  
  CONCLUSIONS
  We identified a set of lncRNAs differentially expressed in gastric cancer, providing useful information for discovery of new biomarkers and therapeutic targets in gastric cancer.
authors.affiliation: Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China.
authors.forename: Wei-Jun
authors.initials: WJ
authors.lastname: Cao
authors.forename: Hai-Lu
authors.initials: HL
authors.lastname: Wu
authors.forename: Bang-Shun
authors.initials: BS
authors.lastname: He
authors.forename: Yu-Shu
authors.initials: YS
authors.lastname: Zhang
authors.forename: Zhen-Yu
authors.initials: ZY
authors.lastname: Zhang
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D019295:Computational Biology; D057225:Data Mining; D030561:Databases, Nucleic Acid; D005091:Exons; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D016014:Linear Models; D009367:Neoplasm Staging; D020411:Oligonucleotide Array Sequence Analysis; D062085:RNA, Long Noncoding / Q000235:genetics*; D015203:Reproducibility of Results; D013274:Stomach Neoplasms / Q000235:genetics* / Q000473:pathology
chemical_list: D014408:Biomarkers, Tumor; D062085:RNA, Long Noncoding
keywords: Data mining; Gastric cancer; Long non-coding RNA; Microarray analysis